[Objective] To analyze the microbiome composition and community characteristics of the foregut, midgut and hindgut of grass carp from different habitats. [Methods] The 16S rRNA high-throughput sequencing technology was applied to analyze the microbial composition and community characteristics of the foregut, midgut and hindgut of grass carp from four habitats, including river, lake, high-density pond culture and low-density reservoir culture. [Results] Venn diagram, Rarefaction Curve and Alpha index showed that microbial diversity of the foregut was higher in the cultured habitats than natural habitats (river and lake), whereas the diversity of the hindgut microbial community had the opposite trend. The microbial composition and community characteristics of the foregut of grass carp in different habitats varied greatly:the dominant microflora in the foregut was Acinetobacter and Cupriavidus in natural habitats, Cetobacterium and Shewanella in high-density culture pond, and Streptococcus and Peptostreptococcus in low-density culture reservoir. [Conclusion] The great differences in foregut microbial composition and community characteristics of grass carp were due to the difference of environmental factors, culture methods and diets. Our findings can provide basic data for the study of intestinal microorganisms of grass carp. There is a potential risk of infection for grass carp in high-density culture habitats, suggesting that the culture density should be controlled as much as possible in the culture of grass carp.